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Introduction to Bioinformatics

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Introduction to Bioinformatics Mesleki İngilizce - Technical English II • Notes: Prof. Dr. Nizamettin AYDIN – In the slides, • texts enclosed by curly parenthesis, {…}, are examples. • texts enclosed by square parenthesis, […], are [email protected] explanations related to examples. http://www.yildiz.edu.tr/~naydin 1 2 Networks Networks • Learning Objectives • Keywords – to acquire basic vocabulary related to network – Connection concepts • In networking, a connection refers to pieces of related information that are transferred through a network – to become familiar with different technologies – Packet – to understanding, the limits, capabilities, and • A packet is the most basic unit that is transferred over a benefits of specific network hardware network. • Sub-areas covered • When communicating over a network, packets are the envelopes that carry your data from one end point to the other – Computer networks – Network Interface – Internet • A network interface can refer to any kind of software interface to networking hardware 3 4 Networks Networks • Keywords • Keywords – LAN • stands for "local area network". – Bandwidth • refers to a network or a portion of a network that is not • the amount of data that can be carried from one point to publicly accessible to the greater internet another in a given time period – WAN • stands for "wide area network". – Topology • means a network that is much more extensive than a LAN. • The physical layout of a network – Protocol – Cryptography • a set of rules and standards that basically define a language that devices can use to communicate. • the study of encryption and decryption. • There are a great number of protocols in use extensively in networking, and they are often implemented in different layers. 5 6 1 Networks Networks-Introduction • Reading text • Comparing a data network to a living organism, • Pre-reading questions – the hardware provides the skeleton or basic infrastructure upon which the nervous system is built. – What is a protocol? • Similarly, a few hundred meters of cable running – Which device forwards packets between networks through the walls of a laboratory is necessary by processing the routing information included in the packet? – but insufficient to constitute a network. – What is called the physical or logical arrangement • Rather, the data pulsing through cables or other of network? media in a coordinated fashion define a network. – Which data communication system spans states, countries, or the whole world? 7 8 Networks-Introduction Networks-Introduction • This coordination is provided by electronics that • The Internet was a natural successor to the cold – connect workstations and shared computer peripherals war projects in the 1950s and early 1960s with the networks – amplify, route, filter, block, and translate data. • The modern Internet was the unintended • An informatics researcher should have a basic outcome of two early complex systems: understanding of the limits, capabilities, and – the ARPANET (Advanced Research Project benefits of specific network hardware, Agency Network) – to be able to converse intelligently with hardware – the SAGE system (semiautomatic ground vendors environment), – to direct the management of an information services • developed for the military in the early 1950s and 1960s, provider. respectively. 9 10 Networks-Introduction Networks-Introduction • SAGE was the national air defense system • The communications network component of the SAGE system was comprehensive and extended beyond the comprised of border of the U.S. and included ships and aircraft. – an elaborate, ad hoc network of incompatible • It was primarily a military system, – with a civil defense link as its only tie with civilian command and control computers, communications system. – early warning radar systems, • In the 1950s and 1960s, federally funded researchers at – weather centers, academic institutions explored ways to manage the growing store of digital data amid the increasingly – air traffic control centers, complex network of computers and networks. – ships, • One development was hypertext, – a cross-referencing scheme, – planes, • where a word in one document is linked to a word in the same or a – weapons systems. different document. 11 12 2 Networks-Introduction Networks-Introduction • Around the time the ARPANET was born, a • In addition to applications for the military, a variety of number of academic researchers began commercial, hypertext-based document management systems were spun out of academia and commercial experimenting with computer-based systems that laboratories, used hypertext. – such as the Owl Guide hypertext program from the University of – For example, in the early 1970s, a team at Carnegie- Kent, England, and Mellon University developed ZOG, – the Notecards system from Xerox PARC in California. • a hypertext-based system that was eventually installed on a • Both of these systems were essentially stand-alone U.S. aircraft carrier. equivalents of a modern Web browser, • ZOG was a reference application that provided the – but based on proprietary document formats with content limited to what could be stored on a hard drive or local area network crew with online documentation that was richly (LAN). cross-linked to improve speed and efficiency of • In this circuitous way, out of the quest for national security locating data relevant to operating shipboard through an indestructible communications network, equipment. – the modern Internet was born. 13 14 Networks-Example Networks-Example • Microarray Laboratory Network • The computers in a typical microarray laboratory present a mixture of – data formats, – operating systems, – processing capabilities. • The network in this example (a wired and wireless local area network) supports – the microarray laboratory processes, • from experimental design and array fabrication to expression analysis and publishing of results. 15 16 Networks Networks • A network architecture should be examined from the perspective of: • Network Taxonomy – Geographical scope – Underlying model or models used to implement the network – Signal transmission technology – Bandwidth or speed – Physical layout or topology – Protocol or standards used to define how signals are handled by the network – Ownership or funding source involved in network development – Hardware, including • cables, wires, and other media used to provide the information conduit from one device to the next – Content carried by the network 17 18 3 Networks Networks • There are multiple networking Technologies: • Geographical Scope – Personal Area Network (PAN) – Local Area Network (LAN) • The geographical extent of a network is – Metropolitan Area Network (MAN) significant because it affects – Wide Area Network (WAN) – bandwidth, – Storage Area Network (SAN) – Enterprise private network (EPN) – security, – Virtual private network (VPN) – response time, – Global Area Network (GAN) – the type of computing possible. – Wireless Local Area Network (WLAN) • For example, it is only because of the high-speed – Controller Area Network (CAN) Internet backbone that real-time teleconferencing and – Internet Area Network (IAN) model sharing are possible on a worldwide basis. 19 20 Networks Networks • Informatics R&D incorporates network resources on worldwide (WAN), • PAN institution-wide (MAN), and laboratory-wide (LAN and PAN) levels. – personal area network • a computer network used for communication among computer devices, – including telephones, personal digital assistants, … • limited to the immediate proximity of the user, or about a 10-meter radius, • If PAN is constructed using wireless technology, – known as wireless personal area network (WPAN) 21 22 Networks Networks • PAN • LAN – local area network • a network that is restricted to smaller physical areas – extend to about 100-meters from a central server, or a single floor in a typical research building. • e.g. a local office, school, or house. • Approximately all current LANs whether wired or wireless are based on Ethernet. • Data transfer speeds can extend to – 10.0 Mbps (Ethernet network) – 1.0 Gbps (Gigabit ethernet) • Coaxial cable and CAT 5 cables are normally used for connection. 23 24 4 Networks Networks • LAN • MAN – Metropolitan Area Network • take over where LANs leave off, – covering entire buildings and extending tens of kilometers. • typically implemented with digital subscriber line (DSL), cable modem, and fixed wireless technologies. • Several LANs are often connected to make a MAN. – When this configuration is used for a college campus, it is referred to as a campus area network (CAN). 25 26 Networks Networks • MAN • WAN – Wide Area Network • connects computers together over large physical distances, – such as entire country or entire world • typically composed of a combination of – terrestrial fixed satellite systems, coaxial cable, and fiber optical cable. • The public switched telephone network and the Internet are examples of WANs. 27 28 Networks Networks • WAN • SAN – Storage area network • connects servers directly to devices to store data • moves storage resources off the common user network and reorganizes them into an independent, high-performance network. – So, each server is allowed to access shared storage. • This can involve Fibre-channel connection, similar to Ethernet, to handle high-performance disk storage for application. 29 30 5 Networks Networks • SAN • EPN – Enterprise Private Network • a computer network built to share computer resources among different sites – such as production sites,
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